Invasion legacy reshapes resident microbiome multifunctionality through the Matthew effect

Abstract Beneficial microbial inoculation is a widely adopted strategy in agriculture for disease suppression and ecosystem service enhancement. However, the invasion and establishment of exogenous strains in soil are often uncertain. Microbial invasions are known to fundamentally alter ecosystem functioning, yet their persistent legacy effects remain inadequately characterized and could pose unintended risks to soil health. Using four taxonomically distinct bacterial inoculants with disease‐suppressive traits, we conducted a longitudinal experiment to trace invasion‐induced community restructuring from the invasion phase through an extended legacy period following invader extinction. Our results, through several bacterial invasions under controlled conditions with varying treatments, reveal a consistent and pronounced ‘Matthew effect’ across all four inoculants, whereby invasion reinforces the dominance of abundant taxa while suppressing rare ones, leading to persistent community polarization and functional trade‐offs. This reorganization enhanced resource acquisition and nutrient cycling but reduced stress tolerance and ecosystem resilience. Mechanistically, invasion legacy accelerates the replacement of slow‐growing with fast‐growing taxa, shifting assembly from deterministic to stochastic processes. This ‘Matthew effect’ was modulated by carbon sources: labile carbon (glucose) intensified polarization, while recalcitrant carbon in organic fertilizer buffered the shift, preserving rare taxa and functional diversity. A supporting analysis of published invasion studies corroborates these patterns, indicating broader ecological relevance. Our findings provide a unifying framework for understanding how transient microbial invasions generate lasting ecological imbalances, cascading from community structure to ecosystem multifunctionality. Importantly, we show that organic amendments, particularly those containing recalcitrant carbon, can mitigate the ‘Matthew effect’ by alleviating resource competition and preserving rare taxa, offering a practical strategy to sustain soil health in bioaugmentation practices.